The Brazilian's goals were separated by a 52nd minute effort from 19-year-old forward Mario Balotelli, who returned to action after being frozen out for a month following a row with coach Jose Mourinho.
Second-placed AS Roma, who stayed in the hunt by beating Inter last week, remain just one point behind thanks to a 1-0 victory at Bari.
AC Milan remained third after snapping a three-match winless streak with a 3-2 victory at Cagliari.
With six matches to go, Inter have 66 points, Roma are on 65 while Milan stayed in contention with 63.
Sampdoria boosted their bid for Italy's final Champions League place when they beat Chievo Verona 2-1 away to pull level on points with fourth-placed Palermo, who lost 2-0 at Sicilian rivals Catania after a Maxi Lopez brace.
Struggling Juventus missed the chance to join them on 51 points when they were thrashed 3-0 at lowly Udinese.
Inter, without suspended quartet Samuel Eto'o, Lucio, Maicon and captain Javier Zanetti, enjoyed most of the possession from the start with Bologna's only real chance coming early on when Adailton hit the post with a freekick.
But, as in Wednesday's 1-0 win over CSKA Moscow in the Champions League quarter-final first leg, they wasted many chances before Motta broke the deadlock with a diagonal shot just before the half hour.
Balotelli, who was included in the team after apologising to Mourinho, sidefooted home to double the lead before Motta sealed the victory with a crisp shot five minutes from time.
COOL FINISH
Roma remain hot on Inter's heels after Mirko Vucinic sprinted on to a Luca Toni pass and produced a cool finish for their winner after 19 minutes.
In Sardinia, Marco Borriello drove the ball into the bottom corner after a one-two with Clarence Seedorf to put Milan in front after seven minutes.
Daniele Ragatzu took advantage of sloppy defending to equalise 10 minutes later but Klaas-Jan Huntelaar responded almost immediately with a splendid long-range left-foot strike.
Alessandro Matri fired Cagliari level again only for defender Davide Astori to hand the advantage back to Milan with a 38th minute own goal.
Juve produced a toothless display and their problems began after nine minutes when Chilean Alexis Sanchez tucked the ball into the net after Antonio Di Natale thumped the post.
Simone Pepe drilled home and Di Natale finished off a nice move in the second half to ease Udinese's relegation worries.
Sixth-placed Napoli's European drive slowed when they were held 1-1 at Lazio.
Atalanta boosted their survival hopes by beating second-bottom Siena 2-0 in a relegation dogfight, leaving them three points behind Lazio and the safety zone.
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